I just don't know how to convert .geojson file to .shp. If you give me an advice I can try to do first method. About second method: I don't know how to implement clipping by geometry.
– SantJun 25 '16 at 13:03

Why can you only use gdal modules, and not console applications?
– BradHardsJun 26 '16 at 4:34

Now the challenge is to extract or read a sub array of this result with the limits of a GeoJson geometry or a shapefile and it is a Numpy problem. For that you need to convert first your limits to pixel offset and size (raster coordinates)

After you have two solutions:

read directly the result (clipped band) with a filter (limits of the geometry);